For a big corporate entity, the general secrecy policy really can work against the efficiency of the company. Apple still manages to make it work, but from what I've seen, things could be so much smoother if people were allowed to be more open with information. Mind you, I'm talking about within the company itself - yes, I've been in plenty of situations where employees in different depts are not allowed to talk directly to each other due to this policy.
Apple tends to be very frugal, for a company with billions in the bank. Salary and equity aside, they don't seem to really hire everywhere that's needed - only on those projects that really have the attention of upper management. Other projects and products, while still producing, suffer from limited resources, and creativity and production is stifled.
There's the usual management hierarchy problems present at any large corporation. At Apple, there tend to be middle managers who have been with Apple a long time, are happy with there lot, and have decided to impede progress for anyone below them. Again, this is typical, but disappointing for a company that claims to 'think different' like Apple.